Nitrogen (N) loss from different benthic habitats via net denitrification and burial was quantified, and first-order N budgets were constructed, for three geomorphically distinct shallow warm temperate South-East Australian barrier estuaries. Seagrass communities were the most important benthic habitats for N loss via net denitrification due to a combination of their area and high denitrification rates. Similarly, the largest N loss via burial occurred in the seagrass communities in the Hastings River Estuary and Wallis Lake, but in contrast, the largest annual loss of N via burial in the Camden Haven occurred in the subtidal muds due to their large area. N inputs to the river-dominated Hasting River Estuary were dominated by diffuse sources from the catchment. Budget deficits in Camden Haven and Wallis Lake suggest that the largest input of N may have been from the ocean, although missing N-fixation and/or groundwater cannot be excluded. Export to the ocean was the largest loss of N in the Hasting River Estuary followed by net denitrification and then burial. Net denitrification was the largest loss of N in the Camden Haven and Wallis Lake followed by burial. As the systems mature (evolve) the burial of N per m2, the loss of N via denitrification per m2 and the % of the total N load that is removed as fish per m2, all decrease. Overall N loss via denitrification for a given residence time may be higher in shallow and oligotrophic coastal systems with extensive seagrass habitats than deeper temperate systems.